[English] 日本語
![](img/lk-miru.gif)
- PDB-7q2i: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7q2i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with Tetrahydrofurfurylamine | ||||||
![]() | Cholinephosphate cytidylyltransferase | ||||||
![]() | TRANSFERASE / Plasmodium Falciparum CCT Inhibitors Fragments | ||||||
Function / homology | ![]() Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / phosphatidylcholine binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Duclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design of PfCCT inhibitors Authors: Duclovel, C. / Gelin, M. / Wein, S. / Wengelnik, K. / Krimm, I. / Guichou, J.F. / Cerdan, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7pveC ![]() 7pvfC ![]() 7pvgC ![]() 7py9C ![]() 7pyaC ![]() 7pybC ![]() 7pycC ![]() 7q2lC ![]() 7q2vC ![]() 7q9vC ![]() 7qa7C ![]() 7qd3C ![]() 7qvnC ![]() 7qvoC ![]() 4zctS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20810.123 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ctP, MAL13P1.86 / Production host: ![]() ![]() References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-GZ6 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 8 Details: PEG 4000 19%, TRIS pH8 0.1M 6-7-8-9-10% Guanidine HCl 5-6-7% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.706→40.714 Å / Num. obs: 17226 / % possible obs: 92.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 39.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.018 / Rrim(I) all: 0.04 / Net I/σ(I): 19.6 / Num. measured all: 91165 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ZCT Resolution: 1.87→40.71 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.16 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.41 Å2 / Biso mean: 51.0757 Å2 / Biso min: 29.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→40.71 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|